Cadmium in PDB 4bpk: Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5

The structure of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5, PDB code: 4bpk was solved by B.J.Smith, E.F.Lee, J.W.Checco, S.H.Gellman, W.D.Fairlie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.066 / 1.76
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	65.175, 72.133, 80.579, 90.00, 90.00, 90.00
R / Rfree (%)	21.92 / 25.22

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Cadmium atom in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 (pdb code 4bpk). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 19 binding sites of Cadmium where determined in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5, PDB code: 4bpk:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1196 b:44.4 occ:0.68 CD A:CD1196 0.0 44.4 0.7 CD A:CD1196 2.0 45.3 0.3 OE2 A:GLU129 2.4 44.7 1.0 O A:HOH2059 2.5 47.2 1.0 CD A:GLU129 3.4 43.6 1.0 OE1 A:GLU129 3.9 40.3 1.0 CB C:ALA7 3.9 43.7 1.0 NH2 C:ARG10 4.0 43.7 1.0 CG A:GLU129 4.7 36.8 1.0

Cadmium binding site 2 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1196 b:45.3 occ:0.32 CD A:CD1196 0.0 45.3 0.3 CD A:CD1196 2.0 44.4 0.7 OE2 A:GLU129 2.4 44.7 1.0 OE1 A:GLU129 2.5 40.3 1.0 CD A:GLU129 2.8 43.6 1.0 O A:HOH2059 3.7 47.2 1.0 CD A:ARG132 3.8 57.7 0.5 NH2 C:ARG10 4.3 43.7 1.0 CG A:GLU129 4.3 36.8 1.0 NE A:ARG132 4.3 60.0 0.5 NE A:ARG132 4.4 60.7 0.5 CG A:ARG132 4.6 59.2 0.5 CG A:ARG132 4.8 57.7 0.5 NH2 A:ARG132 4.8 49.9 0.5 CZ A:ARG132 4.9 56.1 0.5 CD A:ARG132 5.0 61.2 0.5

Cadmium binding site 3 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1197 b:56.4 occ:1.00 O A:HOH2042 2.3 53.8 1.0 OE2 A:GLU92 2.4 44.0 1.0 O A:HOH2043 2.4 55.2 1.0 O A:HOH2023 2.5 43.1 1.0 CD A:GLU92 3.3 46.9 1.0 OE1 A:GLU92 3.6 49.9 1.0 O A:SER18 3.8 40.1 0.7 O A:SER18 3.9 42.8 0.3 NE2 A:GLN88 4.2 36.8 1.0 O A:HOH2008 4.3 61.8 1.0 CG A:GLN88 4.3 35.7 1.0 O A:HOH2035 4.4 38.6 0.4 CG A:GLU92 4.6 41.4 1.0 CD A:GLN88 4.7 38.1 1.0 C A:SER18 4.8 40.2 0.3 C A:SER18 4.8 40.4 0.7 CB A:SER18 5.0 37.0 0.7

Cadmium binding site 4 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1198 b:69.0 occ:1.00 CD2 A:HIS113 2.8 56.7 0.5 NE2 A:HIS113 2.9 56.2 0.5 ND1 A:HIS113 3.2 62.3 0.5 CE1 A:HIS113 3.7 63.0 0.5 CG A:HIS113 4.0 57.9 0.5 CE1 A:HIS113 4.1 56.2 0.5 CG A:HIS113 4.3 62.6 0.5 O A:HOH2066 4.4 57.4 1.0 NZ A:LYS157 4.6 64.7 1.0 ND1 A:HIS113 4.7 52.2 0.5 CB A:HIS113 4.8 60.0 0.5 NE2 A:HIS113 4.9 64.4 0.5

Cadmium binding site 5 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1199 b:46.9 occ:1.00 OE1 A:GLU153 2.3 49.7 1.0 O A:HOH2051 2.4 56.5 1.0 O A:HOH2065 2.4 46.1 1.0 O A:HOH2064 2.4 70.3 1.0 OE2 A:GLU153 2.4 51.0 1.0 O A:HOH2066 2.6 57.4 1.0 CD A:GLU153 2.7 41.0 1.0 CE A:LYS157 4.0 55.6 1.0 CG A:GLU153 4.2 38.0 1.0 O A:HOH2050 4.3 59.3 1.0 O A:LEU112 4.5 58.3 1.0 O A:HOH2063 4.6 42.4 1.0 NZ A:LYS157 4.6 64.7 1.0 OD2 A:ASP156 4.8 52.0 1.0 O A:THR109 4.9 44.1 1.0 CB A:GLU153 5.0 35.0 1.0 O A:SER110 5.0 51.7 1.0

Cadmium binding site 6 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1200 b:62.3 occ:0.45 CD A:CD1200 0.0 62.3 0.5 CD A:CD1200 1.8 64.1 0.6 CE1 A:HIS177 2.6 56.9 0.6 NE2 A:HIS177 3.3 56.3 0.6 CE1 A:HIS177 3.3 56.5 0.4 ND1 A:HIS177 3.7 60.5 0.6 ND1 A:HIS177 4.0 57.4 0.4 NE2 A:HIS177 4.1 55.9 0.4 OD2 A:ASP176 4.3 69.2 0.4 CD2 A:HIS177 4.5 56.0 0.6 CB A:ASP176 4.5 63.8 0.4 CB A:ASP176 4.7 65.2 0.6 CG A:HIS177 4.7 56.5 0.6 OD2 A:ASP176 4.8 70.8 0.6 CG A:ASP176 4.9 67.9 0.4

Cadmium binding site 7 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1200 b:64.1 occ:0.55 CD A:CD1200 0.0 64.1 0.6 CD A:CD1200 1.8 62.3 0.5 CE1 A:HIS177 2.9 56.9 0.6 NE2 A:HIS177 3.1 56.3 0.6 CE1 A:HIS177 3.2 56.5 0.4 NE2 A:HIS177 3.5 55.9 0.4 ND1 A:HIS177 3.8 60.5 0.6 ND1 A:HIS177 4.0 57.4 0.4 CD2 A:HIS177 4.1 56.0 0.6 CD2 A:HIS177 4.4 53.9 0.4 CG A:HIS177 4.5 56.5 0.6 CG A:HIS177 4.7 53.4 0.4

Cadmium binding site 8 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd1201 b:53.8 occ:1.00 O A:HOH2069 2.2 51.0 1.0 O A:HOH2068 2.2 52.7 1.0 OE2 A:GLU179 2.4 61.9 1.0 OE1 A:GLU179 2.7 55.5 1.0 CD A:GLU179 2.9 58.5 1.0 N B:SER2 4.1 68.3 1.0 CG A:GLU179 4.4 54.4 1.0 ND2 B:ASN5 4.6 54.6 1.0 OD1 A:ASN175 4.6 60.7 1.0 CB B:SER2 4.7 84.5 1.0 CA B:SER2 5.0 76.0 1.0

Cadmium binding site 9 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd1196 b:47.5 occ:1.00 OD1 B:ASP189 2.4 67.1 1.0 OD2 B:ASP189 2.4 57.7 1.0 O B:GLY186 2.6 40.8 1.0 CG B:ASP189 2.7 57.8 1.0 O B:HOH2069 2.7 58.9 1.0 C B:GLY186 3.3 40.9 1.0 CA B:GLY186 4.0 44.0 1.0 N B:GLY187 4.1 37.4 1.0 OG1 B:THR190 4.2 50.0 1.0 CB B:ASP189 4.2 53.0 1.0 CA B:GLY187 4.2 32.7 1.0 N B:THR190 4.8 38.5 1.0 C B:GLY187 4.8 36.7 1.0

Cadmium binding site 10 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd1197 b:47.7 occ:1.00 O B:HOH2073 2.3 77.7 1.0 O B:HOH2058 2.3 66.2 1.0 O B:HOH2074 2.4 56.2 1.0 OD2 B:ASP176 2.5 46.0 1.0 OD1 B:ASP176 2.6 46.1 1.0 CG B:ASP176 2.9 43.7 1.0 O B:HOH2061 4.0 59.2 1.0 CG2 B:THR172 4.0 30.1 1.0 CB B:ASP176 4.5 37.4 1.0 O B:HOH2060 4.9 34.8 1.0 O B:THR172 5.0 26.4 1.0

B.J.Smith, E.F.Lee, J.W.Checco, M.Evangelista, S.H.Gellman, W.D.Fairlie. Structure-Guided Rational Design of Alpha/Beta-Peptide Foldamers with High Affinity For Bcl-2 Family Prosurvival Proteins. Chembiochem V. 14 1564 2013.
ISSN: ISSN 1439-4227
PubMed: 23929624
DOI: 10.1002/CBIC.201300351